In a strict sense, the object being descibed has been subject to physical violence. When used as a slang term, the
implication is that the said object is
undesirable or
otherwise crippled.
Strict:
The police roughed up a criminal on drugs before arresting him.
Slang: "John's car is roughed up." This would imply that John's car has many undesirable qualities, eg. old, worn, broken, etc
Slang: If
your grandmother cooked you a
birthday cake and it looked like a lump of sand, you might say that cake is roughed up.